stk.ReplaceFitness

class stk.ReplaceFitness(get_replacement, filter=<function ReplaceFitness.<lambda>>)

Bases: FitnessNormalizer[T]

Replaces fitness values of a certain value with a new value.

Examples

Giving a Fitness Value to Failed Calculations

You want to replace fitness values which are None with half the minimum fitness value in the population. A fitness value may be None because the fitness calculation failed for some reason.

import stk

building_block = stk.BuildingBlock('BrCCBr', stk.BromoFactory())
record1 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
record2 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
fitness_values = {
    record1: 2,
    record2: None,
}

def get_minimum_fitness_value(fitness_values):
    return min(
        value for value in fitness_values.values()
        if value is not None
    )

replacer = stk.ReplaceFitness(
    # The replacement is half the minimum fitness value in the
    # population.
    get_replacement=lambda fitness_values:
        get_minimum_fitness_value(fitness_values) / 2,
    # Only replace fitness values which are None.
    filter=lambda fitness_values, record:
        fitness_values[record] is None,
)

# Use the replacer.
normalized_fitness_values = replacer.normalize(fitness_values)
assert normalized_fitness_values[record1] == 2
assert normalized_fitness_values[record2] == 1

Parameters:

• get_replacement (Callable[[dict[T, Any]], Any]) – Calculates the replacement fitness value. The entire population passed to normalize() is passed to this parameter, regardless of what is passed to the filter parameter.

• filter (Callable[[dict[T, Any], T], bool]) – A function which returns True or False. Only molecules which return True will have fitness values normalized. By default, all molecules will have fitness values normalized. The instance passed to the fitness_values argument of normalize() is passed as the first argument, while the second argument will be passed every MoleculeRecord in it, one at a time.

Methods

normalize

Normalize some fitness values.

normalize(fitness_values)

Normalize some fitness values.

Parameters:

fitness_values (dict[T, Any]) – The molecules which need to have their fitness values normalized.

Returns:

The new fitness value for each molecule.

Return type:

dict[T, Any]